Kevin,
1hps and 1hos do no appear to include Murthy as an author.
Since I need good as well as (very) bad examples for my molecular
modeling teaching,
I spent some time analyzing the structures which pdb codes you provided
with MolProbity.
All score very bad: high B factors, lots of clashes, many Ramachandran
outliers, unfavorable rotamers and bad bond angles.
The lesser bad structures in your list come (surprisingly?) as 1hos and
1hps, but still they are far from optimal.
I have those data available in the case you need them.
I would strongly advise the use of MolProbity (at least) by both
crystallographers and modelers, but also by curators at the rcsb..
Regards,
Nadir
Pr. Nadir T. Mrabet
Cellular & Molecular Biochemistry
INSERM U-954
Nancy University, School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.68.32.73
Fax: +33 (0)3.83.68.32.79
E-mail: [email protected]
Kevin Karplus wrote:
Firas Khatib pointed out that several of the PDB files by Krishna
Murthy's group were identified as problematic in the RosettaHoles paper:
http://www.proteinscience.org/details/journalArticle/110975/RosettaHoles_Rapid_assessment_of_protein_core_packing_for_structure_prediction_r.html
I notice that the RosettaHoles paper also identifies 1BGX as a
problematic file, but that was not listed on the UAB site
http://main.uab.edu/Sites/reporter/articles/71570/
I also notice that most of the identified files have not yet been
marked as obsolete in PDB's "obsolete" file. In fact, only 1BEF was
so marked when I just checked
ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat
Question for the community: should we remove ALL the PDB files from
Krishna Murthy's group as suspect? I find the following in the
current PDB:
listed in article:
1cmw 1df9 2qid 1g40 1g44 1l6l 2ou1 1rid 1y8e 2a01 2hr0
others probably from same author:
1bgx 1ay1 1hef 1heg 1sbg 1hps 1hos
(Incidentally, variations in name abbreviations make it difficult to
be sure that I have found all of the files, or that all of the files
involve the same person.)
Has anyone examined 1bgx, 1ay1, 1hef, 1heg, 1sbg, 1hps, and 1hos to
see if there is any evidence of fraud on those files?
I'm strongly tempted to remove them from my template libraries, unless
I hear from someone who was involved in the investigation that these
files were carefully examined and determined to be ok. The fact that
1bgx was identified by RosettaHoles as suspect makes me wary of just
trusting that silence means they were cleared.
------------------------------------------------------------
Kevin Karplus [email protected] http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
Graduate Director, Bioinformatics
(Senior member, IEEE) (Board of Directors, ISCB)
Editorial Board, Bioinformatics (Oxford University Press)
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